afrimapr/afrilearnr

learning resources for making African maps from data

afrilearnr

A growing collection of interactive learnr tutorials for making African maps.

Online tutorials :

tutorial name	outline	recommended order
intro-to-spatial-r	an introduction to spatial data in R	1
get-my-data-in	getting your own spatial data into R	2
join-admin	dealing with data referenced by names rather than coordinates	3
afrilearnr-crash-course	gallery of plots & code with minimal explanation	4
proposed :
colour-my-map	changing map colours in different map packages
data-manipulation	manipulating your data to allow making different maps
map-my-study-area	making a simple map to show where a study area is

If you would like to suggest a tutorial for this collection, or contribute one, please get in touch.

The tutorials are saved as a package that can also be installed and run locally in RStudio.

Getting started

1. Install the package from GitHub from the R console.

# install.packages("remotes") # if not already installed
remotes::install_github("afrimapr/afrilearnr")

2. Load the package

library(afrilearnr)

3. In RStudio Click on the Tutorial tab at the top right, choose an afrilearnr tutorial, and click Start Tutorial ?

Alternatively you can start a tutorial by name from the R console :

learnr::run_tutorial("join-admin", "afrilearnr")

afrilearnr's Issues

make whole tutorials printable to pdf

To provide a backup option for learners with a poor internet connection we'd like to be able to email them a pdf of the tutorial.

We'd like a solution where we can easily generate a pdf so that we can redo it whenever the tutorial changes (which is frequently in initial development).

Adding print.css from rstudio/learnr#465 to https://github.com/afrimapr/afrilearnr/tree/main/inst/tutorials/intro-to-spatial-r doesn't seem to work.

From Chrome printing the hosted tutorial https://andysouth.shinyapps.io/intro-to-spatial-r to pdf just prints the first topic.

Tutorial tab in RStudio does not list all afrimapr tutorials

Some random tutorials are listed and only the afrilearnr get-my-data-in is available from all the ones that are ready:

This may be related to #8

interactive maps display results of earlier chunks on shinyapps

When the learnr tutorials are hosted on shinyapps, running later chunks can lead to display of the results of earlier chunks using tmap & mapview.

e.g. https://andysouth.shinyapps.io/intro-to-spatial-r/#section-e.-first-maps-with-tmap

Issue does not happen when run locally.

Does happen in a smaller reproducible example :
https://andysouth.shinyapps.io/test-tmap-cache/

About to submit issue to learnr.

Error in intro-to-spatial-r tutorial

Hi @andysouth ,

When running the code for the intro-to-spatial-r tutorial (on a mac):

learnr::run_tutorial("intro-to-spatial-r", "afrilearnr")

I get the following message:

Listening on http://127.0.0.1:4651
Warning: Error in if: argument is of length zero
  72: ui

and this opens in a browser window:

Installation of afrilearnr - no package called learnr

I installed afrilearnr successfully and loaded the library, but when I run

learnr::run_tutorial("join-admin", "afrilearnr")
I get the following:

Error in loadNamespace(name) : there is no package called ‘learnr’

Get-my-data-in execution halted

When running the following code and also when following instructions in the afrilearnr README file I get the error below:

learnr::run_tutorial("get-my-data-in", "afrilearnr")

processing file: get-my-data-in.Rmd
  |.....                                                                                                          |   5%
  ordinary text without R code

  |..........                                                                                                     |   9%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |...............                                                                                                |  14%
  ordinary text without R code

  |....................                                                                                           |  18%
label: packages (with options) 
List of 1
 $ echo: logi TRUE

  |.........................                                                                                      |  23%
  ordinary text without R code

  |..............................                                                                                 |  27%
label: csv-airports (with options) 
List of 2
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE

Quitting from lines 88-104 (get-my-data-in.Rmd) 
Error: '' does not exist in current working directory ('/home/talarify/R/x86_64-pc-linux-gnu-library/4.0/afrilearnr/tutorials/get-my-data-in').

There is no way to recover and try an alternative tutorial if I click on Tutorial -> run tutorial in the tutorial tab. A "Loading tutorial" message appears with a circle that turns continuously and no back/stop button.

I restarted my R session, but the Loading tutorial message stays and wheel keeps on turning.

It works if I right click on the Tutorial tab and click on Reload

join-admin tutorial failing on shinyapps with : Error in value[[3L]](cond) : there is no package called

Runs fine locally. Seems to be an indication of a later error, not the library() part itself.

Found that may be due to fill-in-the-blank sections :
rstudio/learnr#209 (comment)

Suggestion that updating packrat fixes it.

Error in if for join-admin tutorial

Hi,

I just installed afrilearnr and get the following error message when I run:
learnr::run_tutorial("join-admin", "afrilearnr")

Listening on http://127.0.0.1:6081
Warning: Error in if: argument is of length zero
  72: ui

The app opens in the browser - see screenshot

Thanks,

Anelda

errors in join-admin due to packages not being loaded (e.g. dplyr & gapminder)

I think I introduced this bug when fixing the earlier issue with interactive maps.

OGRCreateCoordinateTransformation() returned NULL: PROJ available? from shinyapps when user runs code in intro-to-spatial-r

Recurrence of problem in #2

Occurs because of older versions of spatial packages on shinyapps.io

Resetting the crs of objects is solution. But seemingly doing that earlier in the tutorial doesn't persist ???

sf::st_crs(africapitals) <- 4326

#https://stackoverflow.com/questions/61286108/error-in-cpl-transformx-crs-aoi-pipeline-reverse-ogrcreatecoordinatetrans
#If you save an sf-dataframe with a newer version of GDAL, and then try on a system with an older version of GDAL, the projection info cannot be read properly.
#The solution is to re-set the projection:
#st_crs(data) <- 4326

see r-spatial/sf#1419 (comment)

test deployment to shinyapps.io results in gdal error

processing file: intro-to-spatial-r.Rmd
Quitting from lines 48-62 (intro-to-spatial-r.Rmd)
Error in value[3L] :
OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: local ... tryCatch -> tryCatchList -> tryCatchOne ->
In addition: Warning message:
In CPL_transform(x, crs, aoi, pipeline, reverse) :
GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Execution halted

Online version of intro-to-spatial-r needs rgdal installed

Hi Andy,

When running through https://andysouth.shinyapps.io/intro-to-spatial-r/ and getting to the last section (https://andysouth.shinyapps.io/intro-to-spatial-r/#section-h.-read-spatial-data-from-files), when clicking on Run code the following error comes up:

Cannot create RasterLayer object from this file; perhaps you need to install rgdal first

Same happens in Chrome and Firefox even when I click on Start Over